Deep Learning algorithms (DL) have been applied in different domains such as computer vision, image detection, robotics and speech processing, in most cases, DL demonstrated better performance than the conventional machine learning algorithms (shallow algorithms). The artificial intelligence research community has leveraged the robustness of the DL because of their ability to process large data size and handle variations in biometric data such as aging or expression problem. Particularly, DL research in automatic fingerprint recognition system (AFRS) is gaining momentum starting from the last decade in the area of fingerprint pre-processing, fingerprints quality enhancement, fingerprint feature extraction, security of fingerprint and performance improvement of AFRS. However, there are limited studies that address the application of DL to model fingerprint biometric for different tasks in the fingerprint recognition process. To bridge this gap, this paper presents a systematic literature review and an insightful meta-data analysis of a decade applications of DL in AFRS. Discussion on proposed model’s tasks, state of the art study, dataset, and training architecture are presented. The Convolutional Neural Networks models were the most saturated models in developing fingerprint biometrics authentication. The study revealed different roles of the DL in training architecture of the models: feature extractor, classifier and end-to-end learning. The review highlights open research challenges and present new perspective for solving the challenges in the future. The author believed that this paper will guide researchers in propose novel fingerprint authentication scheme.